It has been previously shown that Lsh can influence de novo methylation of retroviral sequences and endogenous genes, but the precise role of Lsh in the establishment of DNA methylation at a given site remained unclear. We have generated a comprehensive methylation map in Lsh-/- fibroblasts using whole genome bisulfite sequencing in collaboration with Joseph Ecker, Salk Institute. We found that Lsh deletion leads to widespread loss of CG methylation level at uniquely mapped genomic regions. Lsh regulates the establishment of cytosine methylation in a nuclear compartment that is in part defined by Lamin B1 attachment regions. The regions that are affected by Lsh deletion include promoter regions of protein-coding genes and non-coding RNA genes. Despite widespread loss of cytosine methylation at regulatory sequences, RNA polymerase II occupancy and overall transcript levels in the absence of Lsh are similar to those in wild type cells. A subset of promoter regions shows increases of the histone modification H3K27me3 suggesting redundancy of epigenetic silencing mechanisms. Furthermore, we found that Lsh modulates CG methylation at all types of repeat elements (including retrotransposons) and is critical for repression of a subclass of repeats. Altogether, we identified Lsh-/- mice as a unique DNA methylation mutant model, in particular a suitable mammalian model to study biologic consequences of aberrant expression of retrotransposons. We provide a detailed analysis of gene expression changes in relation to DNA methylation alterations, which contributes to our understanding of the biological role of cytosine methylation in development and in disease processes.